Activity for LSDMap

  • Hruska committed [8f3064]

    make new method of including weights in lsdmap ...

  • Eugen Hruska committed [05cf47]

    debug

  • Eugen Hruska committed [2919dd]

    new reweighting

  • Eugen Hruska committed [5f435e]

    save kernel

  • Eugen Hruska committed [b49646]

    p_mdrun uses xtc, it's faster for big proteins

  • Eugen Hruska committed [7bd737]

    new branch new reweighting

  • Eugen Hruska committed [98d6a0]

    save .nc

  • Eugen Hruska committed [bfc1b2]

    rewrote p_mdrun to work on blue-waters

  • Hruska committed [a3963a]

    delete old script

  • Hruska committed [cd0483]

    example dmdmd for ala12

  • Hruska committed [7aca86]

    reweighting print number of simulations in next...

  • Hruska committed [8d0cb7]

    option print kernel

  • Hruska committed [44b6b2]

    new parameter number of eigenvalues in output

  • Hruska committed [44ca04]

    dmdmd prints eg, ev, eps

  • Hruska committed [3c5b9f]

    removed print commands

  • Hruska committed [1a6963]

    new option weight_method

  • J Chen J Chen committed [c3d407]

    added new option 'kneighbor_iw' for finding loc...

  • E H E H posted a comment on ticket #3

    Found a workaround. Just generate a new file with only protein coordinates, no water...

  • E H E H created ticket #3

    water not ignored

  • J Chen J Chen committed [51191c]

    version 2.4

  • J Chen J Chen committed [a8bc8d]

    v2.4 works

  • J Chen J Chen committed [10f286]

    merging dmdmd multiple starting configs from ma...

  • J Chen J Chen committed [d0bb33]

    dmdmd now automatically reads out the number of...

  • J Chen J Chen committed [63ed34]

    remerge with master

  • J Chen J Chen committed [c5706b]

    Using x.y versioning scheme. Version 2.3

  • J Chen J Chen committed [b9a93f]

    Official updates to v2.3.0

  • Chen committed [186569]

    re-added comm.Abort at end of p_mdrun

  • Chen committed [67dbd2]

    minor modifications to p_mdrun

  • J Chen J Chen committed [b410cb]

    merge with branch slurm. Included updates to th...

  • Chen committed [c942e5]

    bug fixes to recent changes

  • J Chen J Chen committed [81fe5d]

    added --version option and options for specifyi...

  • J Chen J Chen committed [349248]

    added --version and -V option to lsdmap

  • J Chen J Chen committed [3d8c42]

    added code for gromacs suffix specification

  • Chen committed [ddd406]

    modified dmdmd bash script to save files on the...

  • Chen committed [fd68dc]

    added comm abort command at the end of each thr...

  • Hruska committed [9834a4]

    nearest neighbor rbffit

  • Hruska committed [da4b6d]

    debug

  • Hruska committed [5f6993]

    debug

  • J Chen J Chen committed [c1ebea]

    changed to saving tmp.gro for preserving H atoms

  • J Chen J Chen committed [2be2a9]

    Merge branch 'master' of https://git.code.sf.ne...

  • J Chen J Chen committed [00816a]

    copy tmp.gro not tmpha.gro to keep hydrogen atoms

  • Hruska committed [84507a]

    added cpuhours log for dmdmd

  • Hruska committed [f9782a]

    add cpuhours log for dmaps

  • Hruska committed [9680e1]

    add cpuhours log for DM-d-MD

  • J Chen J Chen committed [9a347b]

    fixed bugs with neighborlists in lsdmap

  • J Chen J Chen committed [0e9af7]

    fixed bug with idx_neighbor list in lsdmap

  • J Chen J Chen committed [aa09cc]

    fixed bug with neighbor list in lsdmap

  • J Chen J Chen committed [5ed89a]

    bugs

  • J Chen J Chen committed [a5e15e]

    debug

  • Hruska committed [872b77]

    fixed bug in rbf.py

  • J Chen J Chen committed [fc7536]

    use mpirun instead of mpiexec for SLURM

  • Hruska committed [3b0293]

    debug asymmetric option

  • Hruska committed [37b038]

    add option asymmetric

  • J Chen J Chen committed [6eec8d]

    added try clause to copying files, in case they...

  • J Chen J Chen committed [194406]

    fixed number of cores to force to 1

  • J Chen J Chen committed [322152]

    added capability for saving trajectories of a run

  • Hruska committed [84dc28]

    added option kneighbor_invert

  • Hruska committed [ceae92]

    dmdmd with rmsd working

  • Hruska committed [d79231]

    fixed bug: rmsd working again

  • Hruska committed [57956e]

    tica for single trajectory only for stand-alone...

  • Hruska committed [626f35]

    tica for single trajectory only for stand-alone...

  • Hruska committed [cc61ef]

    [lsdmap/rbf.py] Typo on loading embed coordinates

  • Alexander Kluber Alexander Kluber committed [4f6313]

    [lsdmap/rbf.py] Now using coord_reader (alex's ...

  • Alexander Kluber Alexander Kluber committed [125557]

    [lsdmap/rbf.py] Typo on loading embed coordinates

  • Hruska committed [f19712]

    [lsdmap/rbf.py] Now using coord_reader (alex's ...

  • Alexander Kluber Alexander Kluber committed [ec4dc8]

    [lsdmap/rbf.py] Now using coord_reader (alex's ...

  • Hruska committed [b200f4]

    updated lsdmap from Alex

  • Alexander Kluber Alexander Kluber committed [465f1d]

    [lsdmap/rbf.py] Account for RbfFit and RbfExe b...

  • Alexander Kluber Alexander Kluber committed [2f3307]

    [lsdmap/rbf.py] Updated coord reader and distan...

  • Alexander Kluber Alexander Kluber committed [3a1e24]

    Merge branch 'master' of ssh://git.code.sf.net/...

  • EugenHruska committed [320fe7]

    introduced tica option for dmaps

  • Joe Joe committed [9259c5]

    update examples folder and README file

  • Joe Joe committed [a8b074]

    update examples folder and README file

  • Joe Joe committed [7b3c08]

    update examples folder and README file

  • Joe Joe committed [f49203]

    update examples folder and README file

  • Alexander Kluber Alexander Kluber committed [4d02a6]

    [coord_reader.py] Checkouted from master branch

  • Alexander Kluber Alexander Kluber committed [948ab2]

    [setup.py] Removed references to ctram

  • Alexander Kluber Alexander Kluber committed [f06df7]

    [lsdmap.py] Grabbed current version from master...

  • Alexander Kluber Alexander Kluber committed [b58bed]

    dummy removed

  • Alexander Kluber Alexander Kluber committed [6a89d1]

    dummy

  • Alexander Kluber Alexander Kluber committed [bc8ba0]

    Merge branch 'serial' of ssh://git.code.sf.net/...

  • Alexander Kluber Alexander Kluber committed [dbb8a6]

    Merge branch 'serial' of ssh://git.code.sf.net/...

  • Alexander Kluber Alexander Kluber committed [c3f810]

    self.epsilon should be an array

  • Alexander Kluber Alexander Kluber committed [9136c1]

    missing indent

  • Alexander Kluber Alexander Kluber committed [131b1e]

    Alex's new branch

  • Alexander Kluber Alexander Kluber committed [1325fc]

    Alex's new branch

  • Alexander Kluber Alexander Kluber committed [dd2fd6]

    Merge branch 'serial' of ssh://git.code.sf.net/...

  • Alexander Kluber Alexander Kluber committed [fee4c0]

    self.epsilon should be an array

  • Alexander Kluber Alexander Kluber committed [73ec51]

    Merge branch 'serial' of ssh://git.code.sf.net/...

  • Alexander Kluber Alexander Kluber committed [44a355]

    missing indent

  • Joe Joe committed [0c1647]

    fixed issue when the local scale is kneighbor

  • Joe Joe committed [daeeac]

    created serial version of LSDMap

  • Joe Joe committed [1ae247]

    implemented new version of dmaps

  • Joe Joe committed [b9c817]

    Merge branch 'master' of ssh://git.code.sf.net/...

  • Alexander Kluber Alexander Kluber committed [26f38a]

    remove profiler imports

  • Joe Joe committed [61f708]

    back to ctram.c as it is found 3-4 times faster

  • Joe Joe committed [4dfe22]

    changed README file

  • Alexander Kluber Alexander Kluber committed [e7d8a2]

    Merge branch 'dmaps' of ssh://git.code.sf.net/p...

  • J Chen J Chen committed [d28b62]

    allow biasing of coarse-grained models

  • J Chen J Chen committed [842ca7]

    added option for specifying a gromacs suffix

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